The anatomic pathology core, a unit dedicated to the Seattle stem cell transplant program, has supported past research with diagnostic and pathogenetic information on graft-versus-host disease (GVHD), infection, toxicity and engraftment. Pathology support for stem cell transplantation has evolved sufficiently to require several technical disciplines for effective functioning. Therefore, we have updated the core to integrate four areas. Anatomic pathology uses standard methods in addition to immunohistochemistry and in situ hybridization on tissue sections to diagnose infection, GVHD, second tumors and chimerism. Molecular cytogenetics uses fluorescent in situ hybridization to recognize chimerism and tumors. Molecular pathology uses PCR methods to detect minimal residual disease. Multiparameter flow cytometry with sorting provides a highly sensitive method for integrating these findings by detecting small numbers of cells with high sensitivity and specificity. These methods provide key support for every aspect of the grant proposal, including every project and most of the core components, both before and long after transplantation.